This directory contains all the scripts to run the benchmark of the FRETR Bayesian restraint, and the reference results.
GMM: Gaussian Mixture Models needed by model for linker flexibility
PDBs: Pdb with complex structure, one per chain
REFERENCE_RESULTS: reference results of benchmark
SCRIPTS: scripts to run and analyze the benchmark
ANALYSIS: scripts to analyze the results
BENCHMARK_LINKER: scripts to run the benchmark with model for linker flexibility
BENCHMARK_NOLINKER: scripts to run the benchmark without model for linker flexibility
RESULTS_LINKER: directory where the results of benchmark with model for linker flexibility will be stored
RESULTS_NOLINKER: directory where the results of benchmark without model for linker flexibility will be stored
How to run the benchmark
This is the
PRELIMINARY. Compile IMP (any recent version should work - see below for the last known good IMP version). IMP git version develop-c47408c was used for the publication.
EXECUTION. Go to
DATA/SCRIPTS/BENCHMARK_NOLINKERwhere you will find the scripts to run the benchmark with or without using a model for linker flexibility, respectively. Then:
To run a specific test, run:
IDis an integer from 1 to 1280.
To run all tests, just use a bash loop:
for((ID=1;ID<=1280;ID++)); do ./do_test.sh $ID; done
A sample SGE script to run all the tests on a cluster is also provided, as
ANALYSIS. From the
DATA/SCRIPTS/ANALYSIS/do_analysis.py RESULTS_LINKER linker.dat
DATA/SCRIPTS/ANALYSIS/do_analysis.py RESULTS_NOLINKER nolinker.dat
DATA/SCRIPTS/ANALYSIS/do_analysis_per_complex.py RESULTS_LINKER linker_per_complex.dat
DATA/SCRIPTS/ANALYSIS/do_analysis_per_complex.py RESULTS_NOLINKER nolinker_per_complex.dat
Statistics will be written to the
.datfiles, which should be compared to the results in
DATA/REFERENCE_RESULTSand to those published in Bonomi et al. "Determining protein complex structures based on a Bayesian model of in vivo FRET data", as follows.
linker.dat-> Table S2
nolinker.dat-> Table S3
Author(s): Max Bonomi
License: LGPL. This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
- M. Bonomi, E.G. Muller, R. Pellarin, S.J. Kim, D. Russel, R. Ramsden, B.A. Sundin, T.A. Davis, A. Sali. Determining protein complex structures based on a Bayesian model of in vivo FRET data. Mol Cell Proteomics 13, 2812-2823, 2014.